At each interface of liquid and vacuum:
$$\gamma=\int_{-\infty}^{\infty}dz(P_{\perp} - P_{//})$$
$$P_{\perp}=P_{zz},\ P_{//}=\frac{1}{2}(P_{xx}+P_{yy})$$
Since there are two interfaces in the simulation:
$$\gamma=\frac{1}{2} \int_{-\infty}^{\infty} dz\Big[P_{zz}-\frac{1}{2}(P_{xx}+P_{yy})\Big]$$
In [1]:
from polymaps.util import open_lmp_data
_ = open_lmp_data("single_water.data", box=True, unwrap=True)
In [2]:
lmp_input_str = """ # https://github.com/t3rodrig/LammpsTutorials/blob/master/liquid-vapor/in.spce.txt
variable Text equal 300.0 # reference temperature, in K
variable Ndump equal 1000
variable Ndump2 equal 100
units real
boundary p p p
atom_style full
read_data "single_water.data"
include "tip4p2005.ff"
replicate 6 6 6
fix fxshake all shake 0.001 20 0 b 1 a 1
variable xc equal 0.5*(xlo+xhi)
variable yc equal 0.5*(ylo+yhi)
variable zc equal 0.5*(zlo+zhi)
variable xLo equal -0.5*lx
variable xHi equal 0.5*lx
variable yLo equal -0.5*ly
variable yHi equal 0.5*ly
variable zLo equal -2*lz
variable zHi equal 2*lz
displace_atoms all move -${xc} -${yc} -${zc} units box
change_box all x final ${xLo} ${xHi} units box
change_box all y final ${yLo} ${yHi} units box
change_box all z final ${zLo} ${zHi} units box
comm_style tiled
fix fxbalance all balance 100 1.1 rcb
reset_timestep 0
write_data data.long_box.interfaces nocoeff
thermo ${Ndump}
thermo_style custom step dt cpu time temp press density pe ke xlo xhi ylo yhi zlo zhi atoms
thermo_modify flush yes
run 0
"""
with open('in.water.prep', 'w') as lmp_script_file:
lmp_script_file.write(lmp_input_str)
!export OMP_NUM_THREADS=1 && ulimit -s unlimited && mpirun -np 16 /home/xyan11/software/lmp20220623up4/build-cuda/lmp -in in.water.prep
LAMMPS (23 Jun 2022 - Update 4)
using 1 OpenMP thread(s) per MPI task
Reading data file ...
orthogonal box = (2 6.8 1) to (5.1 9.9 4.1)
2 by 2 by 4 MPI processor grid
reading atoms ...
3 atoms
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
2 bonds
reading angles ...
1 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.007 seconds
Replicating atoms ...
orthogonal box = (2 6.8 1) to (20.6 25.4 19.6)
4 by 2 by 2 MPI processor grid
648 atoms
432 bonds
216 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.001 seconds
replicate CPU = 0.002 seconds
Finding SHAKE clusters ...
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
216 = # of frozen angles
find clusters CPU = 0.000 seconds
Displacing atoms ...
Changing box ...
orthogonal box = (-9.3 6.8 1) to (9.3 25.4 19.6)
Changing box ...
orthogonal box = (-9.3 -9.3 1) to (9.3 9.3 19.6)
Changing box ...
orthogonal box = (-9.3 -9.3 -37.2) to (9.3 9.3 37.2)
System init for write_data ...
PPPM initialization ...
extracting TIP4P info from pair style
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.23245361
grid = 15 15 36
stencil order = 5
estimated absolute RMS force accuracy = 0.0027638006
estimated relative force accuracy = 8.3231035e-06
using double precision FFTW3
3d grid and FFT values/proc = 3850 675
WARNING: Communication cutoff 0 is shorter than a bond length based estimate of 3.4358. This may lead to errors. (src/comm.cpp:727)
WARNING: Increasing communication cutoff to 16.1118 for TIP4P pair style (src/KSPACE/pair_lj_cut_tip4p_long.cpp:484)
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 15.3092
ghost atom cutoff = 16.1118
binsize = 7.6546, bins = 3 3 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut/tip4p/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
PPPM initialization ...
extracting TIP4P info from pair style
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.23245361
grid = 15 15 36
stencil order = 5
estimated absolute RMS force accuracy = 0.0027638006
estimated relative force accuracy = 8.3231035e-06
using double precision FFTW3
3d grid and FFT values/proc = 4785 736
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 1
Per MPI rank memory allocation (min/avg/max) = 8.294 | 8.363 | 8.425 Mbytes
Step Dt CPU Time Temp Press Density PotEng KinEng Xlo Xhi Ylo Yhi Zlo Zhi Atoms
0 1 0 0 0 6444.57 0.2510412 1323.8357 0 -9.3 9.3 -9.3 9.3 -37.2 37.2 648
Loop time of 2.91937e-06 on 16 procs for 0 steps with 648 atoms
79.2% CPU use with 16 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Bond | 0 | 0 | 0 | 0.0 | 0.00
Kspace | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 2.919e-06 | | |100.00
Nlocal: 40.5 ave 45 max 36 min
Histogram: 8 0 0 0 0 0 0 0 0 8
Nghost: 2728.5 ave 2772 max 2685 min
Histogram: 8 0 0 0 0 0 0 0 0 8
Neighs: 20992.5 ave 31278 max 11934 min
Histogram: 4 0 0 4 0 4 0 0 0 4
Total # of neighbors = 335880
Ave neighs/atom = 518.33333
Ave special neighs/atom = 2
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00
In [3]:
_ = open_lmp_data("data.long_box.interfaces", box=True, unwrap=True)
In [4]:
lmp_input_str = """ # https://github.com/t3rodrig/LammpsTutorials/blob/master/liquid-vapor/in.spce.txt
variable Nsteps equal 500000 # 2 * 5e5 = 1e6 fs (1 ns). total number of steps in the simulation
variable Nevery equal 100 # use input values every this many timesteps
variable Nfreq equal ${Nsteps}/100 # calculate averages every this many timesteps
variable Nrepeat equal 0.5*v_Nfreq/${Nevery} # calculate averages every this many timesteps
variable Text equal 300.0 # reference temperature, in K
processors 2 2 *
units real
atom_style full
boundary p p p
read_data "data.long_box.interfaces"
include "tip4p2005.ff"
reset_timestep 0
fix fxshake all shake 0.001 20 0 b 1 a 1
timestep 0.5
fix fxnvt all nvt temp ${Text} ${Text} $(150.0*dt)
thermo 1000
thermo_style custom step dt cpu time temp press density pe ke
thermo_modify flush yes
neigh_modify every 1 delay 0 check yes
variable xPress equal c_thermo_press[1]
variable yPress equal c_thermo_press[2]
variable zPress equal c_thermo_press[3]
variable A_in_m equal 1e-10 # Angstrom in meter
variable atm_in_Pa equal 101325 # note: 1 Pa = 1 N/m^2
variable N_in_mN equal 1e3 # Newton in milliNewton
variable convFac equal ${A_in_m}*${atm_in_Pa}*${N_in_mN}
variable st equal 0.5*lz*(v_zPress-0.5*(v_xPress+v_yPress))*${convFac} # in mN/m
fix st all ave/time 50 1 50 v_st file "out.surfTension.txt"
fix strunning all ave/time 1 10 50 v_st ave running file "out.surfTension.running.txt"
variable Dz equal 0.5 # Angstrom
compute CC1 all chunk/atom bin/1d z center ${Dz} units box
fix massDens all ave/chunk ${Nevery} ${Nrepeat} ${Nfreq} CC1 density/mass file "out.massDens.zProfile.txt"
# Computes the symmetric per-atom stress tensor
compute CC2 all chunk/atom bin/1d z center ${Dz} units box
compute stpa all stress/atom NULL
fix stress all ave/chunk ${Nevery} ${Nrepeat} ${Nfreq} CC2 c_stpa[1] c_stpa[2] c_stpa[3] c_stpa[4] c_stpa[5] c_stpa[6] file "out.stress.zProfile.txt"
run ${Nsteps}
write_data "final.liquid-vapor.data" nocoeff
"""
with open('in.water.st', 'w') as lmp_script_file:
lmp_script_file.write(lmp_input_str)
!export OMP_NUM_THREADS=1 && ulimit -s unlimited && mpirun -np 16 /home/xyan11/software/lmp20220623up4/build-cuda/lmp -in in.water.st
LAMMPS (23 Jun 2022 - Update 4)
using 1 OpenMP thread(s) per MPI task
Reading data file ...
orthogonal box = (-9.3 -9.3 -37.2) to (9.3 9.3 37.2)
2 by 2 by 4 MPI processor grid
reading atoms ...
648 atoms
reading velocities ...
648 velocities
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
432 bonds
reading angles ...
216 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.012 seconds
Finding SHAKE clusters ...
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
216 = # of frozen angles
find clusters CPU = 0.000 seconds
PPPM initialization ...
extracting TIP4P info from pair style
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.23245361
grid = 15 15 36
stencil order = 5
estimated absolute RMS force accuracy = 0.0027638006
estimated relative force accuracy = 8.3231035e-06
using double precision FFTW3
3d grid and FFT values/proc = 3136 675
WARNING: Communication cutoff 0 is shorter than a bond length based estimate of 3.4358. This may lead to errors. (src/comm.cpp:727)
WARNING: Increasing communication cutoff to 16.1118 for TIP4P pair style (src/KSPACE/pair_lj_cut_tip4p_long.cpp:484)
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 15.3092
ghost atom cutoff = 16.1118
binsize = 7.6546, bins = 3 3 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut/tip4p/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 0.5
Per MPI rank memory allocation (min/avg/max) = 11.07 | 11.62 | 12.4 Mbytes
Step Dt CPU Time Temp Press Density PotEng KinEng
0 0.5 0 0 0 6446.9697 0.2510412 1323.8357 0
1000 0.5 1.8988723 500 326.15405 113.68336 0.2510412 -2157.1461 419.01961
2000 0.5 3.837713 1000 290.70066 -329.63429 0.2510412 -2230.1147 373.4716
3000 0.5 5.9524021 1500 315.31747 1209.5031 0.2510412 -2320.4296 405.09753
4000 0.5 8.1194657 2000 313.73133 92.644259 0.2510412 -2347.0304 403.05978
5000 0.5 10.156003 2500 308.85914 -423.31355 0.2510412 -2349.7662 396.80033
6000 0.5 12.2971 3000 309.38502 111.23831 0.2510412 -2346.1215 397.47595
7000 0.5 14.354357 3500 291.4911 70.550602 0.2510412 -2314.5708 374.48711
8000 0.5 16.360867 4000 300.01194 -141.83999 0.2510412 -2337.4426 385.43408
9000 0.5 18.357618 4500 305.82869 -119.82348 0.2510412 -2352.0383 392.90702
10000 0.5 20.377916 5000 306.68864 1.5806421 0.2510412 -2334.7095 394.01184
11000 0.5 22.349489 5500 297.30354 -464.10881 0.2510412 -2330.8729 381.95452
12000 0.5 24.287678 6000 279.8737 -384.96631 0.2510412 -2359.035 359.56189
13000 0.5 26.289616 6500 309.70126 -240.67997 0.2510412 -2305.7781 397.88223
14000 0.5 28.272344 7000 300.64799 -172.23182 0.2510412 -2348.9957 386.25123
15000 0.5 30.168319 7500 304.26645 -320.22836 0.2510412 -2348.1253 390.89997
16000 0.5 32.079156 8000 289.80646 158.03393 0.2510412 -2373.2901 372.3228
17000 0.5 34.068744 8500 316.50828 111.21405 0.2510412 -2301.9206 406.6274
18000 0.5 36.099976 9000 296.04551 -464.90048 0.2510412 -2345.9609 380.33829
19000 0.5 38.121885 9500 321.01191 -248.80565 0.2510412 -2341.5889 412.41335
20000 0.5 40.068494 10000 295.40471 108.61233 0.2510412 -2321.6125 379.51503
21000 0.5 42.126572 10500 295.65797 55.352129 0.2510412 -2381.5585 379.8404
22000 0.5 44.109409 11000 305.17056 -331.23592 0.2510412 -2330.0394 392.06151
23000 0.5 46.07561 11500 316.52771 6.1436062 0.2510412 -2342.1554 406.65237
24000 0.5 48.02382 12000 324.10738 -23.222734 0.2510412 -2292.6677 416.39019
25000 0.5 50.012333 12500 305.58038 -82.775644 0.2510412 -2352.6534 392.58802
26000 0.5 52.024089 13000 295.29833 -525.49011 0.2510412 -2347.9708 379.37837
27000 0.5 54.078368 13500 312.63487 -154.62742 0.2510412 -2338.8012 401.65112
28000 0.5 56.035184 14000 296.42451 -18.888134 0.2510412 -2364.0567 380.8252
29000 0.5 58.045052 14500 287.16539 -136.48472 0.2510412 -2368.5948 368.92974
30000 0.5 60.073018 15000 284.13696 -208.54631 0.2510412 -2348.6425 365.03903
31000 0.5 62.132488 15500 301.5834 -215.23025 0.2510412 -2357.9718 387.45297
32000 0.5 64.204968 16000 298.44886 160.89561 0.2510412 -2369.4158 383.42595
33000 0.5 66.284655 16500 287.54571 -251.82445 0.2510412 -2357.4036 369.41835
34000 0.5 68.343033 17000 305.36305 -430.59737 0.2510412 -2360.3065 392.3088
35000 0.5 70.377217 17500 318.76243 -556.06274 0.2510412 -2369.7846 409.52338
36000 0.5 72.325108 18000 305.16525 -205.86878 0.2510412 -2346.2042 392.05469
37000 0.5 74.331589 18500 301.62455 -204.35433 0.2510412 -2293.6575 387.50584
38000 0.5 76.268469 19000 301.83777 -21.626764 0.2510412 -2320.2804 387.77978
39000 0.5 78.311714 19500 286.73488 -376.17842 0.2510412 -2355.8226 368.37665
40000 0.5 80.316598 20000 296.92713 -158.37222 0.2510412 -2366.698 381.47094
41000 0.5 82.242886 20500 297.51723 176.78185 0.2510412 -2401.8342 382.22905
42000 0.5 84.232696 21000 293.26565 -162.33911 0.2510412 -2328.7665 376.76693
43000 0.5 86.175222 21500 295.00308 -489.98876 0.2510412 -2373.8126 378.99904
44000 0.5 88.28265 22000 295.11347 86.287132 0.2510412 -2379.7865 379.14087
45000 0.5 90.34474 22500 280.70977 -137.6175 0.2510412 -2360.3182 360.63602
46000 0.5 92.366397 23000 298.31159 10.768171 0.2510412 -2388.1348 383.2496
47000 0.5 94.408064 23500 271.01086 -167.54042 0.2510412 -2347.1288 348.17554
48000 0.5 96.359307 24000 308.98165 -484.11004 0.2510412 -2334.9417 396.95772
49000 0.5 98.418779 24500 308.80448 151.63381 0.2510412 -2350.6075 396.73011
50000 0.5 100.50456 25000 281.72218 302.94416 0.2510412 -2340.2432 361.9367
51000 0.5 102.563 25500 286.75886 -281.63425 0.2510412 -2333.3901 368.40746
52000 0.5 104.57399 26000 293.85005 -79.413132 0.2510412 -2335.3853 377.51772
53000 0.5 106.59412 26500 278.88766 56.049887 0.2510412 -2329.745 358.2951
54000 0.5 108.63185 27000 296.42967 -101.99893 0.2510412 -2345.6101 380.83184
55000 0.5 110.75608 27500 302.10464 -8.3616605 0.2510412 -2344.2136 388.12263
56000 0.5 112.88541 28000 295.29481 -39.641818 0.2510412 -2328.2324 379.37384
57000 0.5 114.85227 28500 289.93702 -206.33108 0.2510412 -2395.5091 372.49054
58000 0.5 116.89133 29000 295.26286 268.10887 0.2510412 -2309.7862 379.3328
59000 0.5 118.96023 29500 316.2966 -135.69298 0.2510412 -2379.0866 406.35546
60000 0.5 121.01591 30000 308.52044 -291.23407 0.2510412 -2320.9917 396.36519
61000 0.5 122.95205 30500 290.41795 17.698204 0.2510412 -2365.3896 373.1084
62000 0.5 124.97854 31000 288.70666 -62.038342 0.2510412 -2357.6125 370.90985
63000 0.5 127.07015 31500 319.48775 145.91108 0.2510412 -2371.3536 410.45522
64000 0.5 129.16005 32000 315.94514 31.812381 0.2510412 -2353.0776 405.90393
65000 0.5 131.27553 32500 301.21934 -176.34105 0.2510412 -2320.4149 386.98526
66000 0.5 133.26872 33000 319.28294 -326.34936 0.2510412 -2341.909 410.1921
67000 0.5 135.24457 33500 295.90794 113.12029 0.2510412 -2327.2674 380.16154
68000 0.5 137.28207 34000 295.63593 179.99788 0.2510412 -2353.3108 379.81209
69000 0.5 139.31078 34500 313.10321 190.52176 0.2510412 -2381.3185 402.25282
70000 0.5 141.38542 35000 295.64077 -301.25129 0.2510412 -2334.156 379.81831
71000 0.5 143.42506 35500 281.97522 136.35511 0.2510412 -2351.2952 362.26177
72000 0.5 145.45335 36000 292.66779 45.757974 0.2510412 -2351.504 375.99884
73000 0.5 147.46741 36500 295.64154 216.37199 0.2510412 -2349.1133 379.8193
74000 0.5 149.48749 37000 303.09268 -270.60296 0.2510412 -2335.3375 389.392
75000 0.5 151.41467 37500 293.33044 129.85775 0.2510412 -2350.695 376.85017
76000 0.5 153.45876 38000 301.7685 219.23182 0.2510412 -2397.5818 387.69078
77000 0.5 155.40179 38500 327.18909 126.8267 0.2510412 -2335.2851 420.34935
78000 0.5 157.3124 39000 295.51231 -244.4008 0.2510412 -2366.2109 379.65327
79000 0.5 159.23155 39500 286.25837 -394.49639 0.2510412 -2367.6534 367.76447
80000 0.5 161.23523 40000 301.59799 -67.443465 0.2510412 -2359.6454 387.47172
81000 0.5 163.16436 40500 321.16472 -7.5716186 0.2510412 -2327.9584 412.60968
82000 0.5 165.14018 41000 313.48734 -509.8688 0.2510412 -2334.5652 402.74632
83000 0.5 167.11946 41500 304.70325 70.160199 0.2510412 -2347.8805 391.46114
84000 0.5 169.18533 42000 297.14687 220.39521 0.2510412 -2331.0907 381.75324
85000 0.5 171.2014 42500 310.15358 -146.00598 0.2510412 -2360.0949 398.46334
86000 0.5 173.13465 43000 307.159 -224.37967 0.2510412 -2338.9584 394.61612
87000 0.5 175.12882 43500 296.03759 -89.713532 0.2510412 -2351.7866 380.32811
88000 0.5 177.11767 44000 295.33916 -12.477521 0.2510412 -2347.4823 379.43083
89000 0.5 179.113 44500 286.15398 -443.81724 0.2510412 -2359.3805 367.63036
90000 0.5 181.0942 45000 298.23044 -196.04884 0.2510412 -2383.1317 383.14533
91000 0.5 183.07985 45500 301.66228 95.112496 0.2510412 -2429.7645 387.55432
92000 0.5 185.08873 46000 296.45659 -47.114151 0.2510412 -2365.6072 380.86641
93000 0.5 187.07594 46500 294.93012 -51.16554 0.2510412 -2370.6539 378.90532
94000 0.5 189.10332 47000 313.62458 -112.56091 0.2510412 -2399.0613 402.92263
95000 0.5 191.06615 47500 307.15555 -292.57797 0.2510412 -2367.4692 394.61168
96000 0.5 193.06195 48000 290.37677 5.477129 0.2510412 -2357.7862 373.0555
97000 0.5 195.08753 48500 311.89293 -40.792753 0.2510412 -2336.5268 400.69793
98000 0.5 197.06386 49000 317.15414 -503.95735 0.2510412 -2373.2199 407.45717
99000 0.5 199.0878 49500 292.87387 22.456907 0.2510412 -2357.0947 376.26359
100000 0.5 201.09009 50000 304.99669 -317.74891 0.2510412 -2376.5981 391.83814
101000 0.5 203.04352 50500 293.33115 -481.0799 0.2510412 -2331.941 376.85107
102000 0.5 205.03118 51000 294.31665 -370.65243 0.2510412 -2361.813 378.11718
103000 0.5 207.05507 51500 276.45307 -34.673429 0.2510412 -2403.9483 355.16731
104000 0.5 209.06347 52000 309.78755 20.316722 0.2510412 -2316.0227 397.9931
105000 0.5 211.0955 52500 286.90791 -113.60342 0.2510412 -2334.9917 368.59896
106000 0.5 213.07962 53000 297.17669 -217.29792 0.2510412 -2347.5417 381.79155
107000 0.5 215.09601 53500 311.3419 27.982968 0.2510412 -2316.9478 399.99
108000 0.5 217.12928 54000 321.17349 127.47992 0.2510412 -2297.4437 412.62094
109000 0.5 219.14707 54500 300.12769 316.90406 0.2510412 -2375.0735 385.58278
110000 0.5 221.19761 55000 283.9952 -394.98313 0.2510412 -2363.1808 364.85691
111000 0.5 223.20047 55500 290.56781 -140.38803 0.2510412 -2331.8381 373.30093
112000 0.5 225.20079 56000 307.80127 80.842478 0.2510412 -2323.4174 395.44126
113000 0.5 227.27138 56500 295.62517 -77.247638 0.2510412 -2350.8401 379.79827
114000 0.5 229.35346 57000 305.88546 335.03304 0.2510412 -2343.6259 392.97996
115000 0.5 231.39492 57500 298.2418 -120.57398 0.2510412 -2313.1784 383.15993
116000 0.5 233.43432 58000 300.40957 -148.6329 0.2510412 -2388.0913 385.94492
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331000 0.5 668.47178 165500 328.62463 -303.22579 0.2510412 -2358.0639 422.19363
332000 0.5 670.57878 166000 299.82372 122.78415 0.2510412 -2327.1441 385.19227
333000 0.5 672.71894 166500 311.96569 -85.591272 0.2510412 -2344.6226 400.79141
334000 0.5 674.86746 167000 270.73168 -148.53833 0.2510412 -2370.3469 347.81688
335000 0.5 676.81251 167500 309.14725 -42.515084 0.2510412 -2342.8999 397.17047
336000 0.5 678.82033 168000 293.90271 -116.68604 0.2510412 -2340.8201 377.58537
337000 0.5 680.87268 168500 279.60255 -404.30983 0.2510412 -2301.1242 359.21355
338000 0.5 682.91049 169000 292.96379 -368.48595 0.2510412 -2340.2311 376.37911
339000 0.5 684.91352 169500 295.54473 -194.43969 0.2510412 -2367.6974 379.69492
340000 0.5 687.00057 170000 302.99616 310.46646 0.2510412 -2371.3928 389.268
341000 0.5 688.98512 170500 305.8269 -184.30541 0.2510412 -2349.3488 392.90473
342000 0.5 691.0198 171000 309.80272 -333.98808 0.2510412 -2343.6431 398.01257
343000 0.5 693.06614 171500 302.85991 -97.697714 0.2510412 -2328.8459 389.09295
344000 0.5 695.10237 172000 303.03691 -60.200501 0.2510412 -2314.2968 389.32035
345000 0.5 697.11517 172500 282.90573 363.42219 0.2510412 -2302.2404 363.45723
346000 0.5 699.22717 173000 303.61391 -266.5603 0.2510412 -2314.3693 390.06163
347000 0.5 701.27599 173500 313.47153 255.80333 0.2510412 -2364.8487 402.726
348000 0.5 703.35878 174000 320.3658 -483.6989 0.2510412 -2310.7727 411.58328
349000 0.5 705.33638 174500 285.59269 -399.92423 0.2510412 -2347.7734 366.90925
350000 0.5 707.38117 175000 305.05803 -288.13958 0.2510412 -2307.9402 391.91694
351000 0.5 709.37637 175500 300.42639 -159.35042 0.2510412 -2329.0729 385.96654
352000 0.5 711.41366 176000 307.00104 33.483903 0.2510412 -2335.0525 394.41318
353000 0.5 713.39501 176500 286.75628 -12.685011 0.2510412 -2378.4505 368.40415
354000 0.5 715.44013 177000 294.96768 13.932616 0.2510412 -2338.2701 378.95357
355000 0.5 717.48419 177500 319.33786 -270.28166 0.2510412 -2333.9659 410.26265
356000 0.5 719.48353 178000 292.30401 -420.15632 0.2510412 -2307.3424 375.53148
357000 0.5 721.40213 178500 318.13519 -128.86076 0.2510412 -2372.9278 408.71755
358000 0.5 723.43222 179000 299.03902 -124.54924 0.2510412 -2365.2734 384.18414
359000 0.5 725.5237 179500 294.18185 -143.63387 0.2510412 -2305.8214 377.94399
360000 0.5 727.48412 180000 300.97146 -398.06276 0.2510412 -2362.9425 386.66681
361000 0.5 729.56238 180500 306.93423 -366.61982 0.2510412 -2379.6756 394.32735
362000 0.5 731.59556 181000 306.82273 -33.801479 0.2510412 -2350.5762 394.1841
363000 0.5 733.56189 181500 289.98354 -66.588097 0.2510412 -2335.8741 372.5503
364000 0.5 735.49934 182000 302.32361 -202.90538 0.2510412 -2342.7966 388.40395
365000 0.5 737.48369 182500 316.81712 -449.2205 0.2510412 -2370.2497 407.02418
366000 0.5 739.48109 183000 309.03414 134.39744 0.2510412 -2326.3272 397.02516
367000 0.5 741.43584 183500 318.63317 -371.36988 0.2510412 -2288.3718 409.35731
368000 0.5 743.42644 184000 306.56729 -228.75067 0.2510412 -2288.6752 393.85593
369000 0.5 745.31159 184500 297.94285 -177.60919 0.2510412 -2380.0357 382.77586
370000 0.5 747.3072 185000 281.82 -445.88497 0.2510412 -2335.0291 362.06237
371000 0.5 749.22558 185500 307.12523 287.14283 0.2510412 -2329.1974 394.57273
372000 0.5 751.26852 186000 294.86603 -16.743678 0.2510412 -2335.1058 378.82297
373000 0.5 753.29734 186500 293.40844 468.9414 0.2510412 -2350.7391 376.95037
374000 0.5 755.35232 187000 300.24414 -498.73075 0.2510412 -2373.8254 385.73239
375000 0.5 757.40433 187500 286.82203 -41.43045 0.2510412 -2341.0708 368.48862
376000 0.5 759.38629 188000 298.85955 364.17384 0.2510412 -2315.9408 383.95357
377000 0.5 761.42148 188500 299.37468 -164.29694 0.2510412 -2312.3615 384.61538
378000 0.5 763.51247 189000 306.70702 -208.62259 0.2510412 -2322.8205 394.03545
379000 0.5 765.5718 189500 309.82834 -65.673843 0.2510412 -2335.331 398.04549
380000 0.5 767.6206 190000 305.05824 -302.77476 0.2510412 -2336.6395 391.91721
381000 0.5 769.66769 190500 298.44631 130.71641 0.2510412 -2351.2034 383.42267
382000 0.5 771.67471 191000 287.18193 -48.045957 0.2510412 -2362.2906 368.951
383000 0.5 773.70941 191500 287.63173 -280.94261 0.2510412 -2363.9063 369.52887
384000 0.5 775.69503 192000 305.57836 110.54167 0.2510412 -2338.9724 392.58542
385000 0.5 777.67669 192500 293.76803 -168.3968 0.2510412 -2342.9499 377.41235
386000 0.5 779.69826 193000 317.9141 179.18835 0.2510412 -2352.4885 408.43351
387000 0.5 781.73985 193500 292.09992 -57.180807 0.2510412 -2392.2174 375.26927
388000 0.5 783.69848 194000 289.62615 -297.55912 0.2510412 -2352.0926 372.09115
389000 0.5 785.71328 194500 295.46257 -76.747599 0.2510412 -2343.8387 379.58937
390000 0.5 787.74538 195000 311.76618 363.9488 0.2510412 -2382.7519 400.53509
391000 0.5 789.76409 195500 301.41427 -276.57153 0.2510412 -2319.5437 387.23569
392000 0.5 791.73469 196000 297.92854 -167.48052 0.2510412 -2375.2985 382.75747
393000 0.5 793.70357 196500 278.79394 -231.55541 0.2510412 -2365.6848 358.1747
394000 0.5 795.71719 197000 299.41407 -30.723836 0.2510412 -2298.719 384.66598
395000 0.5 797.78119 197500 309.37564 -218.49205 0.2510412 -2297.6302 397.46389
396000 0.5 799.85454 198000 294.70468 -236.78266 0.2510412 -2335.4776 378.61569
397000 0.5 801.85285 198500 302.18903 -649.5122 0.2510412 -2354.4916 388.23106
398000 0.5 803.91325 199000 302.4567 -169.48595 0.2510412 -2325.5027 388.57493
399000 0.5 805.88147 199500 288.43335 -286.4622 0.2510412 -2334.328 370.55873
400000 0.5 807.98523 200000 285.95664 -77.897958 0.2510412 -2337.482 367.37682
401000 0.5 810.0473 200500 314.06809 -155.92974 0.2510412 -2295.5969 403.49243
402000 0.5 811.96914 201000 294.60357 -421.6149 0.2510412 -2308.3958 378.48579
403000 0.5 813.92699 201500 312.98856 -654.41509 0.2510412 -2344.7267 402.10552
404000 0.5 815.84131 202000 299.89882 -159.82442 0.2510412 -2316.4261 385.28875
405000 0.5 817.8858 202500 305.48408 -220.121 0.2510412 -2334.6245 392.4643
406000 0.5 819.89821 203000 307.44205 -123.53578 0.2510412 -2391.7862 394.97975
407000 0.5 821.92824 203500 288.26966 -423.22763 0.2510412 -2298.8127 370.34842
408000 0.5 823.98625 204000 307.62418 -78.788985 0.2510412 -2333.3918 395.21375
409000 0.5 825.99057 204500 292.31351 39.400204 0.2510412 -2324.0972 375.54368
410000 0.5 828.05896 205000 296.58391 -74.124977 0.2510412 -2308.3307 381.02998
411000 0.5 830.03485 205500 305.34985 -140.36375 0.2510412 -2340.0341 392.29185
412000 0.5 832.00788 206000 310.33844 -520.50181 0.2510412 -2372.4006 398.70083
413000 0.5 834.02053 206500 308.84848 -88.849689 0.2510412 -2376.6342 396.78664
414000 0.5 836.05038 207000 306.0045 -69.379595 0.2510412 -2361.9025 393.13289
415000 0.5 838.10931 207500 297.40673 65.432893 0.2510412 -2352.7038 382.08708
416000 0.5 840.18216 208000 298.99543 -148.65989 0.2510412 -2346.4194 384.12813
417000 0.5 842.17383 208500 309.93865 -88.453544 0.2510412 -2349.1523 398.18721
418000 0.5 844.1633 209000 321.58663 -301.95752 0.2510412 -2384.8571 413.15171
419000 0.5 846.22515 209500 293.25722 254.40466 0.2510412 -2389.686 376.75609
420000 0.5 848.26209 210000 288.53478 -313.64547 0.2510412 -2378.7575 370.68904
421000 0.5 850.26856 210500 305.57441 -298.09222 0.2510412 -2352.9728 392.58035
422000 0.5 852.24284 211000 322.33563 238.28736 0.2510412 -2361.1951 414.11398
423000 0.5 854.25538 211500 297.49677 -320.94507 0.2510412 -2325.686 382.20277
424000 0.5 856.27233 212000 302.39074 -48.665272 0.2510412 -2341.4587 388.49019
425000 0.5 858.21924 212500 298.95677 -281.90165 0.2510412 -2361.9166 384.07847
426000 0.5 860.19616 213000 305.80005 -173.49981 0.2510412 -2329.6216 392.87023
427000 0.5 862.18232 213500 285.74473 -94.18132 0.2510412 -2335.6855 367.10458
428000 0.5 864.17155 214000 286.82519 -338.58188 0.2510412 -2315.3916 368.49267
429000 0.5 866.21408 214500 302.18182 -207.99002 0.2510412 -2328.4646 388.22179
430000 0.5 868.3026 215000 295.59308 -31.618059 0.2510412 -2316.9656 379.75704
431000 0.5 870.3281 215500 299.21309 -126.85078 0.2510412 -2313.3575 384.40778
432000 0.5 872.32378 216000 311.0957 -195.96663 0.2510412 -2309.0066 399.6737
433000 0.5 874.40938 216500 312.18908 221.30335 0.2510412 -2290.0235 401.07841
434000 0.5 876.41087 217000 291.08776 -242.13366 0.2510412 -2306.5634 373.96893
435000 0.5 878.34092 217500 302.49809 -55.412313 0.2510412 -2339.1061 388.62811
436000 0.5 880.3528 218000 304.64803 -152.92816 0.2510412 -2338.5731 391.39021
437000 0.5 882.33364 218500 302.10429 65.976399 0.2510412 -2328.0505 388.12218
438000 0.5 884.25145 219000 287.39326 -177.49265 0.2510412 -2336.5423 369.22249
439000 0.5 886.19868 219500 304.40844 -6.3730061 0.2510412 -2301.9957 391.08239
440000 0.5 888.21832 220000 291.45794 60.365379 0.2510412 -2331.3333 374.44451
441000 0.5 890.28349 220500 292.37314 63.013239 0.2510412 -2356.1161 375.62029
442000 0.5 892.31753 221000 292.23248 240.82979 0.2510412 -2389.3043 375.43958
443000 0.5 894.4383 221500 306.89167 -313.29366 0.2510412 -2367.4256 394.27267
444000 0.5 896.52345 222000 289.7248 55.825309 0.2510412 -2362.529 372.21789
445000 0.5 898.51568 222500 316.2522 -502.77396 0.2510412 -2332.7463 406.29842
446000 0.5 900.40679 223000 311.90712 -319.3222 0.2510412 -2338.2992 400.71616
447000 0.5 902.24063 223500 294.83143 -92.968016 0.2510412 -2337.643 378.77853
448000 0.5 904.20136 224000 302.04898 129.73741 0.2510412 -2317.4793 388.05113
449000 0.5 906.24308 224500 304.66373 209.48837 0.2510412 -2399.1591 391.41037
450000 0.5 908.36923 225000 299.11123 129.6679 0.2510412 -2398.3829 384.27692
451000 0.5 910.43683 225500 312.92359 -340.34195 0.2510412 -2354.3015 402.02205
452000 0.5 912.51645 226000 301.3135 263.5912 0.2510412 -2378.8173 387.10623
453000 0.5 914.54443 226500 305.55603 -410.92249 0.2510412 -2344.0822 392.55673
454000 0.5 916.58902 227000 277.3972 53.967141 0.2510412 -2331.3964 356.38026
455000 0.5 918.56125 227500 279.53148 -200.00891 0.2510412 -2330.7656 359.12224
456000 0.5 920.56622 228000 296.05772 -86.131568 0.2510412 -2327.9934 380.35397
457000 0.5 922.58285 228500 295.04743 -94.928488 0.2510412 -2334.0121 379.05603
458000 0.5 924.62903 229000 304.88658 83.894047 0.2510412 -2363.4314 391.69667
459000 0.5 926.65585 229500 282.79297 -289.72213 0.2510412 -2353.8448 363.31237
460000 0.5 928.70138 230000 304.23618 -4.7058686 0.2510412 -2323.3758 390.86108
461000 0.5 930.70743 230500 284.13792 -71.417293 0.2510412 -2346.9857 365.04026
462000 0.5 932.73467 231000 306.70383 -33.393949 0.2510412 -2359.9111 394.03135
463000 0.5 934.74229 231500 305.89805 -278.36284 0.2510412 -2353.1035 392.99613
464000 0.5 936.69522 232000 307.43663 -203.79988 0.2510412 -2351.477 394.9728
465000 0.5 938.76552 232500 294.57766 399.95888 0.2510412 -2377.1584 378.45251
466000 0.5 940.73194 233000 320.72159 -218.2239 0.2510412 -2370.3282 412.04036
467000 0.5 942.73643 233500 301.40956 -347.7791 0.2510412 -2357.8788 387.22964
468000 0.5 944.69417 234000 296.43909 -449.36598 0.2510412 -2370.07 380.84393
469000 0.5 946.67848 234500 302.48119 -175.98449 0.2510412 -2353.5847 388.60639
470000 0.5 948.71702 235000 284.57697 -177.52455 0.2510412 -2372.0123 365.60432
471000 0.5 950.7053 235500 313.35107 -233.04087 0.2510412 -2357.0482 402.57124
472000 0.5 952.69782 236000 301.12588 -55.2905 0.2510412 -2387.8119 386.86519
473000 0.5 954.68603 236500 271.62268 -236.95567 0.2510412 -2422.4778 348.96156
474000 0.5 956.71697 237000 296.5734 7.7218161 0.2510412 -2337.2659 381.01649
475000 0.5 958.76654 237500 316.00279 -307.27994 0.2510412 -2384.6625 405.97799
476000 0.5 960.76835 238000 292.34738 -227.723 0.2510412 -2363.8624 375.5872
477000 0.5 962.72324 238500 319.27202 -459.19274 0.2510412 -2365.4521 410.17807
478000 0.5 964.68167 239000 297.66593 -224.76104 0.2510412 -2374.742 382.42009
479000 0.5 966.6102 239500 320.26952 13.510396 0.2510412 -2322.8568 411.45959
480000 0.5 968.57287 240000 295.87394 -118.05157 0.2510412 -2327.4419 380.11787
481000 0.5 970.48177 240500 291.34095 -158.50661 0.2510412 -2353.7761 374.2942
482000 0.5 972.47212 241000 292.13741 252.86888 0.2510412 -2374.3772 375.31744
483000 0.5 974.39234 241500 290.81476 -378.54436 0.2510412 -2367.0209 373.6182
484000 0.5 976.37994 242000 282.5588 60.328566 0.2510412 -2370.043 363.01152
485000 0.5 978.3843 242500 298.95968 -70.587296 0.2510412 -2329.5512 384.08221
486000 0.5 980.36651 243000 295.21992 113.0129 0.2510412 -2315.1651 379.27763
487000 0.5 982.40632 243500 307.65447 -40.407068 0.2510412 -2307.5488 395.25266
488000 0.5 984.45472 244000 309.42831 -13.263708 0.2510412 -2319.8898 397.53156
489000 0.5 986.53204 244500 287.01617 20.514467 0.2510412 -2315.8842 368.73804
490000 0.5 988.62785 245000 305.22188 48.221767 0.2510412 -2363.5284 392.12744
491000 0.5 990.64804 245500 315.28264 -144.59661 0.2510412 -2366.5822 405.0528
492000 0.5 992.67041 246000 285.5711 -361.35256 0.2510412 -2360.3481 366.88152
493000 0.5 994.74337 246500 318.88016 224.21804 0.2510412 -2384.1523 409.67463
494000 0.5 996.80593 247000 285.15678 -197.00372 0.2510412 -2318.7325 366.34923
495000 0.5 998.88187 247500 290.82004 58.220766 0.2510412 -2362.7503 373.62498
496000 0.5 1000.8755 248000 283.23881 306.64422 0.2510412 -2355.5564 363.88515
497000 0.5 1002.9438 248500 296.3843 -181.0755 0.2510412 -2410.9491 380.77354
498000 0.5 1004.9334 249000 325.79508 -0.72532548 0.2510412 -2331.6413 418.55844
499000 0.5 1006.8686 249500 324.02026 38.829907 0.2510412 -2340.1084 416.27827
500000 0.5 1008.8697 250000 288.75984 133.95157 0.2510412 -2302.151 370.97818
Loop time of 1008.87 on 16 procs for 500000 steps with 648 atoms
Performance: 21.410 ns/day, 1.121 hours/ns, 495.604 timesteps/s
98.9% CPU use with 16 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.062537 | 175.04 | 678.9 |2161.2 | 17.35
Bond | 0.068083 | 0.11894 | 0.14217 | 7.2 | 0.01
Kspace | 225.96 | 727.21 | 916.96 |1056.8 | 72.08
Neigh | 10.219 | 10.506 | 11.055 | 10.0 | 1.04
Comm | 2.593 | 37.674 | 50.752 | 330.1 | 3.73
Output | 0.068895 | 0.084161 | 0.10907 | 5.1 | 0.01
Modify | 39.694 | 53.626 | 76.008 | 179.5 | 5.32
Other | | 4.617 | | | 0.46
Nlocal: 40.5 ave 155 max 0 min
Histogram: 12 0 0 0 0 0 0 0 0 4
Nghost: 2147.81 ave 3097 max 0 min
Histogram: 4 0 0 0 0 0 0 0 5 7
Neighs: 20557.2 ave 82569 max 0 min
Histogram: 12 0 0 0 0 0 0 0 1 3
Total # of neighbors = 328915
Ave neighs/atom = 507.58488
Ave special neighs/atom = 2
Neighbor list builds = 9425
Dangerous builds = 0
System init for write_data ...
PPPM initialization ...
extracting TIP4P info from pair style
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.23245361
grid = 15 15 36
stencil order = 5
estimated absolute RMS force accuracy = 0.0027638006
estimated relative force accuracy = 8.3231035e-06
using double precision FFTW3
3d grid and FFT values/proc = 3136 675
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Total wall time: 0:16:48
In [5]:
_ = open_lmp_data("final.liquid-vapor.data", box=True, unwrap=False)
In [6]:
!ls -lrt out.*
-rwxrwxrwx 1 xyan11 xyan11 149871 Aug 23 20:02 out.surfTension.txt -rwxrwxrwx 1 xyan11 xyan11 146732 Aug 23 20:02 out.surfTension.running.txt -rwxrwxrwx 1 xyan11 xyan11 285995 Aug 23 20:02 out.massDens.zProfile.txt -rwxrwxrwx 1 xyan11 xyan11 586559 Aug 23 20:02 out.stress.zProfile.txt
In [7]:
import pandas as pd
import numpy as np
from polymaps.util import read_lmp_fix_file
stepsize = 0.5 / 1000
args = read_lmp_fix_file("out.massDens.zProfile.txt")
df = pd.concat(args["dfs"], axis=0)
df["timestep"] = np.repeat(np.array(args["Timestep"]), args["Number-of-chunks"])
df["time_ps"] = df["timestep"] * stepsize
import plotly.express as px
fig = px.scatter(df, x="Coord1", y="density/mass", animation_frame="time_ps", height=600)
fig.update_xaxes(title="Z coordinate (Å)")
fig.update_yaxes(title="Density (g/cm^3)")
fig.update_layout(title="Density vs. Z coordinate")
fig.show()
In [8]:
args = read_lmp_fix_file("out.stress.zProfile.txt")
_df = pd.concat(args["dfs"], axis=0)
_df["timestep"] = np.repeat(np.array(args["Timestep"]), args["Number-of-chunks"])
_df["time_ps"] = _df["timestep"] * stepsize
_df.columns = _df.columns[:3].tolist() + ["xx", "yy", "zz", "xy", "xz", "yz"] + _df.columns[9:].tolist()
df = _df.melt(id_vars=['Chunk', 'Coord1', 'Ncount', 'timestep', 'time_ps'],
value_vars=["xx", "yy", "zz", "xy", "xz", "yz"])
fig = px.scatter(df,
x="Coord1", y="value",
animation_frame="time_ps", color="variable",
height=600)
fig.update_xaxes(title="Z coordinate (Å)")
fig.update_yaxes(title="Stress (atm)")
fig.update_layout(title="Stress vs. Z coordinate")
fig.show()
In [9]:
df = pd.read_csv("out.surfTension.running.txt", skiprows=2, sep=r"\s+", names=["Timestep", "Surface Tension (mN/m)"])
df["time_ps"] = df["Timestep"] * stepsize
fig = px.line(df, x="time_ps", y="Surface Tension (mN/m)", height=600)
fig.update_xaxes(title="Simulation Time (ps)")
fig.update_yaxes(title="Surface Tension (mN/m)")
fig.update_layout(title="Surface Tension vs. Time")
fig.show()
In [10]:
str(df.at[len(df)-1, "Surface Tension (mN/m)"]) + " mN/m"
Out[10]:
'67.3071 mN/m'
In [ ]:
In [ ]: